Sulawesi is the largest, most topographically complex island in the Wallacean biogeographic zone, and it has a rich fauna of endemic small mammals, dominated by rodents of the family Muridae. Among murids, the Bunomys division is the most species‐rich radiation on Sulawesi. In total, the division contains 11 genera and 32 species, five and 20 of which are endemic to Sulawesi. We combined a five‐locus phylogeny and linear cranial morphology to better understand the taxonomy and local scales of endemism within the Bunomys division on Sulawesi. Phylogenetic analyses of mitochondrial and nuclear DNA placed B. fratrorum among other genera and inferred Paruromys as sister to the type species of Taeromys (T. celebensis). We resolve these issues by resurrecting Frateromys, a genus under which B. fratrorum was once placed, and returning Paruromys dominator to Taeromys. Within three species, F. fratrorum, T. callitrichus, and T. taerae, we recovered Pleistocene age divergences between populations sampled across the northern peninsula of Sulawesi; divergence between western and eastern populations of F. fratrorum may reflect the existence of two species. [ABSTRACT FROM AUTHOR]